[gmx-users] Lipid bilayer parameters

[David]

On Sat, 2005-07-23 at 05:20 -0700, naga raju wrote:
> Dear gmx-users,
>                 I built a lipid bilayer (72 lipid
> molecules and 2376 water molecules) by taking one
> lipid molecule from the dppc.pdb file in website:
> http://moose.bio.ucalgary.ca/index.php?page=Downloads
>  I downloaded dppc.itp and lipid.itp files from the
> above link. when i used the grompp command, it shows
> the following error. 
> 
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C1 - C2)
this is bad.
fix your top or pdb file such that they match.

> Warning: atom names in dppc.top and bbww.pdb don't
> match (C2 - N4)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (N4 - C5)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C5 - C6)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C6 - O7)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (O7 - P8)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (P8 - O9)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (O9 - O10)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (O10 - O11)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (O11 - C12)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C12 - C13)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C13 - O14)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (O14 - C15)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C15 - O16)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (O16 - C17)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C17 - C18)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C18 - C19)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C19 - C20)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C20 - C21)
> Warning: atom names in dppc.top and bbww.pdb don't
> match (C21 - C22)
> (more than 20 non-matching atom names)
> WARNING 1 [file "dppc.top", line 26]:
>   9096 non-matching atom names
>   atom names from dppc.top will be used
>   atom names from bbww.pdb will be ingnored
>  
> double-checking input for internal consistency...
> ERROR: One of the box vectors is shorter than twice
> the cut-off length. Increase the box size or decrease
> rlist.
> There was 1 warning
> 
> 
> How can be the problem solved?
> Here i gave my dppc.top file:
> 
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "dppc.itp"
> #include "alm.itp"
> #include "ions.itp"
> 
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> 
> [ system ]
> ; name
> Alm on surf + relaxed popc
> 
> [ molecules ]
> ; name	number
> DPPC    72
> SOL     2376
> 
> 
>                  Thank you
>                                   nagaraju
> 
> 
> 
> 		
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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